Merge branch 'f-extern2' into 'dev'

MAINT: further tests and docs

See merge request !19

CHANGELOG.md

@@ -31,7 +31,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
   h5py is now an optional dependency
 - table importer implementations for csv and tsv
 - string-in-list check for table imports
-* AbtractCFood has new property, `update_flags`.
+- AbtractCFood has new property, `update_flags`.
 
 ### Changed ###
 

integrationtests/insert_model.py

@@ -5,18 +5,29 @@ from caosadvancedtools.cfoods.h5 import H5CFood
 from caosadvancedtools.models.data_model import DataModel
 from caosadvancedtools.models.parser import parse_model_from_yaml
 
-model = parse_model_from_yaml("model.yml")
-model.sync_data_model(noquestion=True)
-
-if len(db.execute_query("FIND Property alias")) == 0:
-    al = db.Property(name="alias")
-    al.add_parent(name="name")
-    al.insert()
-
-h5model = db.Container()
-h5file = h5py.File('extroot/ExperimentalData/2010_TestProject/2019-02-03/hdf5_dummy_file.hdf5', 'r')
-H5CFood.create_structure(h5file, create_recordTypes=True, collection=h5model,
-                         root_name="ExampleH5")
-print(h5model)
-h5model = DataModel(h5model)
-h5model.sync_data_model(noquestion=True)
+
+def main():
+
+    # for testing existing data model parts with the YAML Interface
+    db.RecordType(name="TestRT1", datatype=db.TEXT).insert()
+    db.Property(name="TestP1", datatype=db.TEXT).insert()
+
+    model = parse_model_from_yaml("model.yml")
+    model.sync_data_model(noquestion=True)
+
+    if len(db.execute_query("FIND Property alias")) == 0:
+        al = db.Property(name="alias")
+        al.add_parent(name="name")
+        al.insert()
+
+    h5model = db.Container()
+    h5file = h5py.File(
+        'extroot/ExperimentalData/2010_TestProject/2019-02-03/hdf5_dummy_file.hdf5', 'r')
+    H5CFood.create_structure(h5file, create_recordTypes=True, collection=h5model,
+                             root_name="ExampleH5")
+    h5model = DataModel(h5model)
+    h5model.sync_data_model(noquestion=True)
+
+
+if __name__ == "__main__":
+    main()

integrationtests/model.yml

@@ -69,3 +69,6 @@ Report:
   - Publication
 hdf5File:
   datatype: REFERENCE
+extern:
+  - TestRT1
+  - TestP1

integrationtests/test_crawl_with_datamodel_problems.py

@@ -34,6 +34,8 @@ from caosadvancedtools.models.parser import parse_model_from_yaml
 from caosadvancedtools.scifolder import (AnalysisCFood, ExperimentCFood,
                                          PublicationCFood, SimulationCFood)
 
+from insert_model import main as insert_model
+
 
 def setup_module():
     """Clear problems and remove all entities except for built-in ones."""
@@ -67,8 +69,7 @@ def test_crawler_with_data_model_problems():
                            prefix="", dryrun=False, forceAllowSymlinks=False)
 
     # load and damage the model
-    model = parse_model_from_yaml("model.yml")
-    model.sync_data_model(noquestion=True)
+    insert_model()
     deleted_entities = {"Experiment", "Poster", "results"}
 
     for ent in deleted_entities:

src/doc/yaml_interface.rst

@@ -39,6 +39,9 @@ Let's start with an example taken from https://gitlab.indiscale.com/caosdb/src/c
           table:
              datatype: FILE
              description: 'A table document associated with this recording'
+    extern:
+       - Textfile
+
 
 
 This example defines 3 ``RecordType``s:
@@ -46,6 +49,9 @@ This example defines 3 ``RecordType``s:
 - A ``Project`` with one obligatory property ``datatype``
 - A Person with a ``firstName`` and a ``lastName`` (as recommended properties)
 - A ``LabbookEntry`` with multiple recommended properties of different data types
+- It is assumed that the server knows a RecordType or Property with the name 
+  "Textfile".
+
 
 One major advantage of using this interface (in contrast to the standard python interface) is that properties can be defined and added to record types "on-the-fly". E.g. the three lines for ``firstName`` as sub entries of ``Person`` have two effects on CaosDB:
 
@@ -60,6 +66,8 @@ Note the difference between the three property declarations of ``LabbookEntry``:
 - ``responsible``: This defines and adds a property with name "responsible" to ``LabbookEntry`, which has a datatype ``Person``. ``Person`` is defined above.
 - ``firstName``: This defines and adds a property with the standard data type ``TEXT`` to record type ``Person``.
 
+If the data model depends on already existing parts, those can be added using the ``extern`` keyword.
+
 Datatypes
 ---------